LECTURE
1. An overview of the use of molecular modeling on specific major publications, with emphasis on state-of-the-art approaches.
2. Computer simulations vs. experiment. Model building, data interpretation, validation of results.
3. Classical models: Molecular mechanics. Concept of force field, contributions to force field, binding and non-binding interactions, parameterization.
4. Classical Dynamics: Equations of motion and their integration, concept of barostats, thermostats, periodic boundary conditions, steps to successful molecular dynamics simulation setup, simulation protocols.
5. Introduction to modeling from first principles.
6. Introduction to semiempirical methods.
PRACTICAL PART
1. Building and visualizing molecular structures of chemical and biological systems using commonly used programs. Formats for writing system coordinates, molecule topology.
2. Short simulation of molecular dynamics of chemical/biological systems.
3. Calculation of the potential energy surface of small systems. Optimization vs. single point calculations.
4. Adsorption of molecules on the surface of low-dimensional structures.
5. Intermolecular complexes - stability, interaction energy, self-assembly.
6. Calculation of frequencies and thermodynamic quantities.
7. Modelling spectra of molecular systems (UV-Vis, CD, ...).
1. An overview of the use of molecular modeling on specific major publications, with emphasis on state-of-the-art approaches.
2. Computer simulations vs. experiment. Model building, data interpretation, validation of results.
3. Classical models: Molecular mechanics. Concept of force field, contributions to force field, binding and non-binding interactions, parameterization.
4. Classical Dynamics: Equations of motion and their integration, concept of barostats, thermostats, periodic boundary conditions, steps to successful molecular dynamics simulation setup, simulation protocols.
5. Introduction to modeling from first principles.
6. Introduction to semiempirical methods.
PRACTICAL PART
1. Building and visualizing molecular structures of chemical and biological systems using commonly used programs. Formats for writing system coordinates, molecule topology.
2. Short simulation of molecular dynamics of chemical/biological systems.
3. Calculation of the potential energy surface of small systems. Optimization vs. single point calculations.
4. Adsorption of molecules on the surface of low-dimensional structures.
5. Intermolecular complexes - stability, interaction energy, self-assembly.
6. Calculation of frequencies and thermodynamic quantities.
7. Modelling spectra of molecular systems (UV-Vis, CD, ...).